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README.md

Kleborate container

Main tool : Kleborate 2.4.1

Additional tools:

  • kaptive 2.0.8
  • ncbi-blast+ 2.9.0
  • mash 2.3
  • python 3.8.2
  • biopython 1.81

Full documentation: https://github.com/katholt/Kleborate/wiki

Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:

  • MLST sequence type
  • species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
  • ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
  • virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
  • antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
  • K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

Why is there staphb/kleborate:2.3.2 and staphb/kleborate:2.3.2-2023-05? What is the difference?

A small change was made to the Kleborate v2.3.2 dockerfile to account for an odd UID (1081147385) and GID (1360859114) that owns the mash executable and license file. This can cause problems in "rootless" environments or environments where docker is run inside of a docker container such as in GitPod. These environments have more limits placed on UIDs and GIDs than your typical linux computers. Error shown below:

$ docker pull staphb/kleborate:2.3.2
2.3.2: Pulling from staphb/kleborate
47c764472391: Pull complete 
f1582e59f07e: Pull complete 
a2c96ce05542: Pull complete 
213b944f2044: Pull complete 
e136842d98e3: Extracting [==================================================>]  1.847MB/1.847MB
d99354f29fdd: Download complete 
499193a95fe3: Download complete 
4f4fb700ef54: Download complete 
failed to register layer: ApplyLayer exit status 1 stdout:  stderr: failed to Lchown "/mash-Linux64-v2.3/LICENSE.txt" for UID 1081147385, GID 1360859114 (try increasing the number of subordinate IDs in /etc/subuid and /etc/subgid): lchown /mash-Linux64-v2.3/LICENSE.txt: invalid argument

The dockerfile now has a step to chown these files so that the root user owns them, which prevents these odd errors.

The updated docker image is available under the docker image name: staphb/kleborate:2.3.2-2023-05

Example Usage

# run Kleborate on assembly supplied with Kleborate code
kleborate --resistance --kaptive --all \
        --assemblies /Kleborate/test/test_genomes/172.fasta.gz \
        --outfile /data/strain172-kleborate-test-out.tsv